SMARTSViewer
StreamableVernalis custom KNIME nodes package version 1.12.0.v201708101336 by Vernalis (R&D), UK
K. Schomburg, H.-C. Ehrlich, K. Stierand, M.Rarey; From Structure Diagrams to Visual Chemical Patterns, J. Chem. Inf. Model., 2010, 50, pp 1529-1535
The Communication Error Settings tab allows setting of behaviour relating to server communication problem handling. The values set are applied to each row in turn. The server will only be contacted until a successful result is returned. The settings allow the user to control the behaviour of the node should the SMARTSviewer server be functioning incorrectly. Note that it is not currently possible to cancel execution during a row, so use long delay settings with care!
Note that SMARTs strings are transferred to the remote server unencrypted, and the the server maintains an anonymous record of query SMARTs strings to aid future development.
This node was developed by Vernalis (Cambridge, UK). For feedback and more information, please contact knime@vernalis.com
Options
- Select a column containing the SMARTs Strings
- Select a column containing SMARTs strings for visualsation. No SMARTS validation is carried out prior to sending to the remote server, which will return a blank image for invalid SMARTS strings
- Select legend type
- Choose the desired legend type: Dynamic - detailed text description of each atom and bond; Static - short description of how each symbol is depicted in the visualisation
- Select Visualisation modus
- Element symbols uses text representation of the element symbols in the depiction
Communication Error Settings
- Number of retries to contact server
- Set the number of times the server will be re-contacted following a failure.
- Delay between attempts (secs)
- The delay period between each re-try
- Ignore server errors
- If set, the node will return a 'missing value' cell for each row which failed to contact the server after the defined number of attempts - allowing workflow execution to continue, otherwise node execution will fail. Setting a long delay interval (max 10 minutes) and large number of attempts (max 20) allows the workflow a chance to restore functionality (it will take over 3 hours between the first and last attempt for each row in these circumstances)
- Restore Defaults
- Restore the default server settings.
Input Ports
Output Ports
Best Friends (Incoming)
- File Reader (13 %) Streamable
- Molecule Type Cast (13 %) Streamable
- MarvinSketch (8 %)
- CSV Reader (8 %)
- Table Creator (8 %)
- Random Numbers Generator (4 %) Streamable
- SMARTSViewer (4 %) Streamable
- MolConverter (4 %) Streamable
- Row Filter (4 %) Streamable
- Column Rename (4 %) Streamable
- Smiles Directory Reader (4 %)
Excel Reader (XLS)(4 %) StreamableDeprecated- Ring Descriptors (4 %)
- RDKit Canon SMILES (4 %) Streamable
- RDKit MCS (4 %)
- RDKit From Molecule (4 %)
- RDKit Find Murcko Scaffolds (4 %) Streamable
- Show all 17 recommendations
Best Friends (Outgoing)
- Interactive Table (local) (21 %)
- SDF Writer (11 %)
- SMARTS Query (11 %)
- Empty Column Checker (5 %)
- SMARTSViewer (5 %) Streamable
K Nearest Neighbor(5 %) StreamableDeprecated- Reference Column Filter (5 %) Streamable
- Molecule Type Cast (5 %) Streamable
- Table to PDF (5 %)
- Excel Writer (XLS) (5 %)
- PNG Image to ImgPlus (5 %) Streamable
- RDKit Molecule Highlighting (5 %) Streamable
- RDKit Interactive Table (5 %)
- RDKit From Molecule (5 %)
- Show all 14 recommendations
Workflows
Installation
To use this node in KNIME, install Vernalis custom KNIME nodes package from the following update site: